3SVM Transferase date Jul 12, 2011
title Human Mpp8 - Human Dnmt3ak47me2 Peptide
authors Y.Chang, J.R.Horton, X.Zhang, X.Cheng
compound source
Molecule: M-Phase Phosphoprotein 8
Chain: A
Fragment: Unp Residues 55-116
Synonym: Two Hybrid-Associated Protein 3 With Ranbpm, Twa3
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mphosph8, Mpp8
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pxc941

Molecule: Dna (Cytosine-5)-Methyltransferase 3a
Chain: P
Fragment: Unp Residues 40-53
Synonym: Dnmt3a, Dna Methyltransferase Hsaiiia, Dna Mtase H M.Hsaiiia;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: I 2 2 2
R_factor 0.257 R_Free 0.272
length a length b length c angle alpha angle beta angle gamma
41.090 43.900 90.280 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.31 Å
ligand MLY enzyme Transferase E.C. BRENDA
Primary referenceMPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a., Chang Y, Sun L, Kokura K, Horton JR, Fukuda M, Espejo A, Izumi V, Koomen JM, Bedford MT, Zhang X, Shinkai Y, Fang J, Cheng X, Nat Commun. 2011 Nov 15;2:533. doi: 10.1038/ncomms1549. PMID:22086334
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (17 Kb) [Save to disk]
  • Biological Unit Coordinates (3svm.pdb1.gz) 13 Kb
  • Biological Unit Coordinates (3svm.pdb2.gz) 25 Kb
  • LPC: Ligand-Protein Contacts for 3SVM
  • CSU: Contacts of Structural Units for 3SVM
  • Structure Factors (54 Kb)
  • Retrieve 3SVM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3SVM from S2C, [Save to disk]
  • Re-refined 3svm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3SVM in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3SVM
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3SVM, from MSDmotif at EBI
  • Fold representative 3svm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3svm] [3svm_P] [3svm_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3SVM: [CHROMO ] by SMART
  • Other resources with information on 3SVM
  • Community annotation for 3SVM at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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